Impact of Teat Order on Feed Consumption in Swine from Birth to Nursery

A relationship between teat order and feed consumption has been assumed in pigs, but no study has looked at this exact relationship. Pigs were observed shortly after birth to be in either a cranial, middle, or caudal teat positon. Growth performance data and active and total plasma ghrelin concentrations were analyzed at birth, weaning, and at the end of the nursery stage of production to see if a relationship with teat order was present. Overall, no effect of teat order was found on average daily gain, average daily feed intake, gain-to-feed ratio, or body weight among pigs from each section of the udder. Differences did occur during certain stages of nursery, which can be of economic importance to producers. No difference was seen in active or total ghrelin levels or the active-to-total ghrelin ratio in relation to teat order, although there were differences in active and total ghrelin concentrations among the sampling days. Further research should be carried out to investigate what factors would contribute to this data contradicting previous inferences about the relationship of teat order and feed consumption in pigs

Degradable starch nanoparticle assisted ethanol precipitation of DNA

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.carbpol.2014.04.007 © 2014. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Precipitation of DNA from a large volume of aqueous solution is an important step in many molecular biology and analytical chemistry experiments. Currently, this is mainly achieved by ethanol precipitation, where a long-term incubation (usually overnight) at low temperature of −20 to −80 °C with high salt concentration is required. This method also requires a large quantity of DNA to form a visible pellet and was tested mainly for double-stranded DNA. To improve DNA precipitation, co-precipitating polymers such as linear polyacrylamide has been used. In this work, we report that starch nanoparticles (SNPs) can achieve convenient DNA precipitation at room temperature with a low salt concentration and short incubation time. This method requires as low as 0.01–0.1% SNPs and can precipitate both single- and double-stranded DNA of various lengths. The effect of salt concentration, pH and the crosslinking density of SNPs has been systematically studied. Compared to other types of precipitating agents, SNPs are highly biocompatible and can be degraded by a common enzyme (amylase). This work suggests a novel application of a bio-based material that is prepared in mass production.Natural Sciences and Engineering Research Council || EcoSynthetix Inc. |

Degradable starch nanoparticle assisted ethanol precipitation of DNA

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.carbpol.2014.04.007 © 2014. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Precipitation of DNA from a large volume of aqueous solution is an important step in many molecular biology and analytical chemistry experiments. Currently, this is mainly achieved by ethanol precipitation, where a long-term incubation (usually overnight) at low temperature of −20 to −80 °C with high salt concentration is required. This method also requires a large quantity of DNA to form a visible pellet and was tested mainly for double-stranded DNA. To improve DNA precipitation, co-precipitating polymers such as linear polyacrylamide has been used. In this work, we report that starch nanoparticles (SNPs) can achieve convenient DNA precipitation at room temperature with a low salt concentration and short incubation time. This method requires as low as 0.01–0.1% SNPs and can precipitate both single- and double-stranded DNA of various lengths. The effect of salt concentration, pH and the crosslinking density of SNPs has been systematically studied. Compared to other types of precipitating agents, SNPs are highly biocompatible and can be degraded by a common enzyme (amylase). This work suggests a novel application of a bio-based material that is prepared in mass production.Natural Sciences and Engineering Research Council || EcoSynthetix Inc. |

Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency

<p>Abstract</p> <p>Background</p> <p>Investigation of metagenomes provides greater insight into uncultured microbial communities. The improvement in sequencing technology, which yields a large amount of sequence data, has led to major breakthroughs in the field. However, at present, taxonomic binning tools for metagenomes discard 30-40% of Sanger sequencing data due to the stringency of BLAST cut-offs. In an attempt to provide a comprehensive overview of metagenomic data, we re-analyzed the discarded metagenomes by using less stringent cut-offs. Additionally, we introduced a new criterion, namely, the evolutionary conservation of adjacency between neighboring genes. To evaluate the feasibility of our approach, we re-analyzed discarded contigs and singletons from several environments with different levels of complexity. We also compared the consistency between our taxonomic binning and those reported in the original studies.</p> <p>Results</p> <p>Among the discarded data, we found that 23.7 ± 3.9% of singletons and 14.1 ± 1.0% of contigs were assigned to taxa. The recovery rates for singletons were higher than those for contigs. The <it>Pearson </it>correlation coefficient revealed a high degree of similarity (0.94 ± 0.03 at the phylum rank and 0.80 ± 0.11 at the family rank) between the proposed taxonomic binning approach and those reported in original studies. In addition, an evaluation using simulated data demonstrated the reliability of the proposed approach.</p> <p>Conclusions</p> <p>Our findings suggest that taking account of conserved neighboring gene adjacency improves taxonomic assignment when analyzing metagenomes using Sanger sequencing. In other words, utilizing the conserved gene order as a criterion will reduce the amount of data discarded when analyzing metagenomes.</p

Three-dimensional endoscopic optical coherence tomography imaging of cervical inlet patch

A 30-year-old white man with established Barrett’s esophagus (BE) and continued symptoms of chronic severe heartburn, persistent cough, throat irritation, and asthma was referred for surveillance EGD at the VA Boston Healthcare System. During retraction of the endoscope, a pink circular lesion (A) was observed under white light endoscopy in the upper esophagus (spanning 20–22 cm from the incisors). Three-dimensional endoscopic optical coherence tomography (OCT) images were obtained of the region under direct visualization with white light by passing the probe through the standard accessory channel. An en face projection image (B) at 400-μm depth underneath the tissue surface showed columnar epithelium consistent with a cervical inlet patch (CIP) and surrounding normal squamous epithelium (SE). Cross-sectional OCT images along the probe pull-back direction (C) and the probe rotation direction (D and F) clearly demonstrated columnar and squamous epithelium in the CIP region and the surrounding esophagus, respectively. Biopsy specimens taken from the imaged lesion confirmed the finding of CIP. The OCT features matched representative hematoxylin and eosin histology (E and G). Both esophageal and extraesophageal symptoms responded to increased antacid therapy.United States. Veterans AdministrationNational Institutes of Health (U.S.) (Grant R01-CA75289-14)United States. Air Force Office of Scientific Research (Contract FA9550-10-1-0063)United States. Dept. of Defense. Medical Free Electron Laser Program (Contract FA9550-10-1-0551)MIT/Center for Integration of Medicine and Innovative Technology (Medical Engineering Fellowship)National Science Council of Taiwan (Taiwan Merit Scholarship

Comparison of Tissue Architectural Changes between Radiofrequency Ablation and Cryospray Ablation in Barrett’s Esophagus Using Endoscopic Three-Dimensional Optical Coherence Tomography

Two main nonsurgical endoscopic approaches for ablating dysplastic and early cancer lesions in the esophagus have gained popularity, namely, radiofrequency ablation (RFA) and cryospray ablation (CSA). We report a uniquely suited endoscopic and near-microscopic imaging modality, three-dimensional (3D) optical coherence tomography (OCT), to assess and compare the esophagus immediately after RFA and CSA. The maximum depths of architectural changes were measured and compared between the two treatment groups. RFA was observed to induce 230~260  m depth of architectural changes after each set of ablations over a particular region, while CSA was observed to induce edema-like spongiform changes to ~640 μm depth within the ablated field. The ability to obtain micron-scale depth-resolved images of tissue structural changes following different ablation therapies makes 3D-OCT an ideal tool to assess treatment efficacy. Such information could be potentially used to provide real-time feedback for treatment dosing and to identify regions that need further retreatment.National Institutes of Health (U.S.) (Grant R01-CA75289-15)National Institutes of Health (U.S.) (Grant K99-EB010071-01A1)National Institutes of Health (U.S.) (Grant R44-CA101067-06)United States. Air Force Office of Scientific Research (Contract FA9550-10-1-0063)Medical Free Electron Laser Program (Contract FA9550-10-1-0551

Characterization of buried glands before and after radiofrequency ablation by using 3-dimensional optical coherence tomography (with videos)

Background Radiofrequency ablation (RFA) is an endoscopic technique used to eradicate Barrett's esophagus (BE). However, such ablation can commonly lead to neosquamous epithelium overlying residual BE glands not visible by conventional endoscopy and may evade detection on random biopsy samples. Objective To demonstrate the capability of endoscopic 3-dimensional optical coherence tomography (3D-OCT) for the identification and characterization of buried glands before and after RFA therapy. Design Cross-sectional study. Setting Single teaching hospital. Patients Twenty-six male and 1 female white patients with BE undergoing RFA treatment. Interventions 3D-OCT was performed at the gastroesophageal junction in 18 patients before attaining complete eradication of intestinal metaplasia (pre–CE-IM group) and in 16 patients after CE-IM (post–CE-IM group). Main Outcome Measurements Prevalence, size, and location of buried glands relative to the squamocolumnar junction. Results 3D-OCT provided an approximately 30 to 60 times larger field of view compared with jumbo and standard biopsy and sufficient imaging depth for detecting buried glands. Based on 3D-OCT results, buried glands were found in 72% of patients (13/18) in the pre–CE-IM group and 63% of patients (10/16) in the post–CE-IM group. The number (mean [standard deviation]) of buried glands per patient in the post–CE-IM group (7.1 [9.3]) was significantly lower compared with the pre–CE-IM group (34.4 [44.6]; P = .02). The buried gland size (P = .69) and distribution (P = .54) were not significantly different before and after CE-IM. Limitations A single-center, cross-sectional study comparing patients at different time points in treatment. Lack of 1-to-1 coregistered histology for all OCT data sets obtained in vivo. Conclusion Buried glands were frequently detected with 3D-OCT near the gastroesophageal junction before and after radiofrequency ablation.National Institutes of Health (U.S.) (Grant R01-CA75289-15)National Institutes of Health (U.S.) (Grant R44CA101067-06)National Institutes of Health (U.S.) (Grant R01-HL095717-03)National Institutes of Health (U.S.) (Grant R01-NS057476-05)National Institutes of Health (U.S.) (Grant K99-EB010071-01A1)United States. Air Force Office of Scientific Research (Contract FA9550-10-1-0063)United States. Air Force Office of Scientific Research. Medical Free Electron Laser Program (Contract FA9550-10-1-0551)Center for Integration of Medicine and Innovative Technolog

Structural markers observed with endoscopic 3-dimensional optical coherence tomography correlating with Barrett's esophagus radiofrequency ablation treatment response

Background Radiofrequency ablation (RFA) is effective for treating Barrett's esophagus (BE) but often involves multiple endoscopy sessions over several months to achieve complete response. Objective Identify structural markers that correlate with treatment response by using 3-dimensional (3-D) optical coherence tomography (OCT; 3-D OCT). Design Cross-sectional. Setting Single teaching hospital. Patients Thirty-three patients, 32 male and 1 female, with short-segment (<3 cm) BE undergoing RFA treatment. Intervention Patients were treated with focal RFA, and 3-D OCT was performed at the gastroesophageal junction before and immediately after the RFA treatment. Patients were re-examined with standard endoscopy 6 to 8 weeks later and had biopsies to rule out BE if not visibly evident. Main Outcome Measurements The thickness of BE epithelium before RFA and the presence of residual gland-like structures immediately after RFA were determined by using 3-D OCT. The presence of BE at follow-up was assessed endoscopically. Results BE mucosa was significantly thinner in patients who achieved complete eradication of intestinal metaplasia than in patients who did not achieve complete eradication of intestinal metaplasia at follow-up (257 ± 60 μm vs 403 ± 86 μm; P < .0001). A threshold thickness of 333 μm derived from receiver operating characteristic curves corresponded to a 92.3% sensitivity, 85% specificity, and 87.9% accuracy in predicting the presence of BE at follow-up. The presence of OCT-visible glands immediately after RFA also correlated with the presence of residual BE at follow-up (83.3% sensitivity, 95% specificity, 90.6% accuracy). Limitations Single center, cross-sectional study in which only patients with short-segment BE were examined. Conclusion Three-dimensional OCT assessment of BE thickness and residual glands during RFA sessions correlated with treatment response. Three-dimensional OCT may predict responses to RFA or aid in making real-time RFA retreatment decisions in the future.Center for Integration of Medicine and Innovative Technology (Medical Engineering Fellowship)United States. Dept. of Veterans Affairs. Boston Healthcare SystemNational Institutes of Health (U.S.) (Grant R01-CA75289-15)National Institutes of Health (U.S.) (Grant R44CA101067-06)National Institutes of Health (U.S.) (Grant K99-EB010071-01A1)United States. Air Force Office of Scientific Research (Grant FA9550-10-1-0063)United States. Air Force Office of Scientific Research. Medical Free Electron Laser Program (Grant FA9550-10-1-0551

Recent advances in MEMS-VCSELs for high performance structural and functional SS-OCT imaging

Since the first demonstration of swept source optical coherence tomography (SS-OCT) imaging using widely tunable micro-electromechanical systems vertical cavity surface-emitting lasers (MEMS-VCSELs) in 2011, VCSEL-based SSOCT has advanced in both device and system performance. These advances include extension of MEMS-VCSEL center wavelength to both 1060nm and 1300nm, improved tuning range and tuning speed, new SS-OCT imaging modes, and demonstration of the first electrically pumped devices. Optically pumped devices have demonstrated continuous singlemode tuning range of 150nm at 1300nm and 122nm at 1060nm, representing a fractional tuning range of 11.5%, which is nearly a factor of 3 greater than the best reported MEMS-VCSEL tuning ranges prior to 2011. These tuning ranges have also been achieved with wavelength modulation rates of >500kHz, enabling >1 MHz axial scan rates. In addition, recent electrically pumped devices have exhibited 48.5nm continuous tuning range around 1060nm with 890kHz axial scan rate, representing a factor of two increase in tuning over previously reported electrically pumped MEMS-VCSELs in this wavelength range. New imaging modes enabled by optically pumped devices at 1060nm and 1300nm include full eye length imaging, pulsatile Doppler blood flow imaging, high-speed endoscopic imaging, and hand-held wide-field retinal imaging.National Institutes of Health (U.S.) (Grant R44EY022864-01)National Institutes of Health (U.S.) (Grant R44EY022864-02)National Institutes of Health (U.S.) (Grant R44CA101067-05)National Institutes of Health (U.S.) (Grant R44CA101067-06)National Institutes of Health (U.S.) (Grant R44CA101067-07)National Institutes of Health (U.S.) (Grant R01-EY011289-26)National Institutes of Health (U.S.) (Grant R01-CA075289-15)National Institutes of Health (U.S.) (Grant R01-EY013178-12)National Institutes of Health (U.S.) (Grant R01-EY013516-09)National Institutes of Health (U.S.) (Grant R01-EY018184-05)National Institutes of Health (U.S.) (Grant R01-NS057476-05)United States. Air Force Office of Scientific Research (Grant FA9550-10-1-0551)United States. Air Force Office of Scientific Research (Grant FA9550-12-1-0499)Thorlabs, Inc

Frequency comb swept lasers

We demonstrate a frequency comb (FC) swept laser and a frequency comb Fourier domain mode locked (FC-FDML) laser for applications in optical coherence tomography (OCT). The fiber-based FC swept lasers operate at a sweep rate of 1kHz and 120kHz, respectively over a 135nm tuning range centered at 1310nm with average output powers of 50mW. A 25GHz free spectral range frequency comb filter in the swept lasers causes the lasers to generate a series of well defined frequency steps. The narrow bandwidth (0.015nm) of the frequency comb filter enables a ~-1.2dB sensitivity roll off over ~3mm range, compared to conventional swept source and FDML lasers which have −10dB and −5dB roll offs, respectively. Measurements at very long ranges are possible with minimal sensitivity loss, however reflections from outside the principal measurement range of 0-3mm appear aliased back into the principal range. In addition, the frequency comb output from the lasers are equally spaced in frequency (linear in k-space). The filtered laser output can be used to self-clock the OCT interference signal sampling, enabling direct fast Fourier transformation of the fringe signals, without the need for fringe recalibration procedures. The design and operation principles of FC swept lasers are discussed and designs for short cavity lasers for OCT and interferometric measurement applications are proposed.National Institutes of Health (U.S.) (R01-CA75289-12)National Institutes of Health (U.S.) (R01-EY011289-24)United States. Air Force Office of Scientific Research (FA9550-07-1-0014)United States. Dept. of Defense. Medical Free Electron Laser Program (FA9550-07-1-0101)National Science council of Taiwan. Taiwan Merit ScholarshipCenter for Integration of Medicine and Innovative Technolog